The cytoscape platform, if you've downloaded and installed the application, would allow you to do that. In short, you would

1) import a network (from NDex or file or list) if you use NDex you can look for a network with "STRING" and whatever your biological system is. If you have a small list you can also copy and paste your accession list.

2) import a table from file,. This would be your excel sheet with accession with fold change, pvalues etc. Essentially your experiment

3) In the style tab you would then go to label, and select the column containing your proteins/genes. Select mapping type as continuous (this allows you to make downregulated blue and upregulated red for eg)

4) GO to the select tab: Column Filter and select your fold-change column and set your cut-off e.g. log2 (1) for a 2-fold change. So it will only show proteins/genes that are upregulated by 2-fold or more.

5) You can use 'apps' if you wanted to generate networks based on GO annotations as well.

The manual http://manual.cytoscape.org/en/3.7.1/ describes it in better detail.

1)Download the interactions from string in excel format

2) create a separate excel sheets where the first column will be all upregulated proteins and 2nd colomn will be all the downregulated proteins.

3) import the first excel sheet to cytoscape

4) select all the upregulated proteins from the first column of excel sheet in no 2, search them in cytoscape. Go to table panel- add new column and assign a value 1 to all of them. Repeat the process for downregulated proteins anc assign them 2.

Go to style- node- select discreteapping. And assign two separate color for both of them.